He was prosecuted within the statute of limitations for the crime, and probably not too far out of the normal bounds between a criminal act and a federal prosecution. Federal prosecutions are relatively rare compared to state prosecutions, federal prosecutors don't take nearly as many "flyers" as states do, and the feds very often wait a long time before pouncing; this is all consistent with their M.O.

In this particular case, I don't disagree that there was probably motivation to the prosecution! They probably did want something from Rockenhaus, and, when they didn't get it straight up, looked for leverage. Unfortunately for Rockenhaus, he had given them a lot of leverage. It looks like it was a lay-up case.

You can call that a moral grey area and I won't disagree, but my point is just, it's not remotely a legal grey area. Rockenhaus' experience of this prosecution is probably no different than that of a typical federal defendant.